8B5H

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH (R)-7-((R)-1,2-dihydroxyethyl)-1,3-dimethyl-5-(1-methyl-1H-pyrazol-4-yl)-1,3-dihydro-2H-benzo[d]azepin-2-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29330% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.829α = 90
b = 52.503β = 90
c = 32.04γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002015-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.632.0696.70.02040.99942.15.215964
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6979.90.0750.978143.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEin house1.60332.061591576896.3380.1590.15740.179319.452
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.13-0.2130.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.663
r_dihedral_angle_4_deg23.719
r_dihedral_angle_3_deg12.816
r_lrange_it5.391
r_lrange_other5.389
r_dihedral_angle_1_deg4.528
r_scangle_it2.737
r_scangle_other2.736
r_mcangle_it1.808
r_mcangle_other1.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.663
r_dihedral_angle_4_deg23.719
r_dihedral_angle_3_deg12.816
r_lrange_it5.391
r_lrange_other5.389
r_dihedral_angle_1_deg4.528
r_scangle_it2.737
r_scangle_other2.736
r_mcangle_it1.808
r_mcangle_other1.808
r_scbond_it1.622
r_scbond_other1.621
r_angle_other_deg1.252
r_angle_refined_deg1.166
r_mcbond_it1.066
r_mcbond_other1.063
r_nbd_refined0.199
r_nbd_other0.165
r_nbtor_refined0.164
r_symmetry_nbd_other0.161
r_symmetry_nbd_refined0.115
r_xyhbond_nbd_refined0.094
r_symmetry_xyhbond_nbd_refined0.08
r_symmetry_nbtor_other0.079
r_chiral_restr0.062
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms923
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling